A B C D E F G H I J K L M N O P Q R S T U V W X Z

C

calculateArrayLength(long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList

Calculates the number of long array elements necessary to store the specified number of elements.

calculateBitsPerValue(int) - Static method in class info.bioinfweb.commons.collections.PackedIntegerArrayList

Calculates how many bits are necessary to represent the specified number of different values.

canRedo() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit

canUndo() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit

CaptchaDBManagement - Class in info.bioinfweb.commons.servlet

CaptchaDBManagement(SQLManipulator, String, String, int, String, int) - Constructor for class info.bioinfweb.commons.servlet.CaptchaDBManagement

cascade(int) - Method in class info.bioinfweb.commons.swing.ExtendedDesktopPane

cascade() - Method in class info.bioinfweb.commons.swing.ExtendedDesktopPane

changedUpdate(DocumentEvent) - Method in class info.bioinfweb.commons.swing.SwingChangeMonitor

ChangeMonitor - Class in info.bioinfweb.commons.changemonitor

Basic implementation of ChangeMonitorable.

ChangeMonitor() - Constructor for class info.bioinfweb.commons.changemonitor.ChangeMonitor

ChangeMonitorable - Interface in info.bioinfweb.commons.changemonitor

A common interface that can be implemented by classes that track whether they have undergone changes.

CHAR_SET_COMMAND - Static variable in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser

CharacterStateSetType - Enum in info.bioinfweb.commons.bio

Enumerates defined token set definitions (e.g.

CharacterSymbolMeaning - Enum in info.bioinfweb.commons.bio

Enumerates defined meanings of single character states in sequence alignments.

CharacterSymbolType - Enum in info.bioinfweb.commons.bio

Enumerates of which type a character symbol may be.

charSequenceToStringList(CharSequence) - Static method in class info.bioinfweb.commons.text.StringUtils

Converts the specified character sequence to a list strings, where each character of the sequence is represented as a single string object.

CharSet - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus

Stores a label of a part of a sequence (e.g.

CharSet(String) - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.CharSet

CharSetNexusFileBuilder - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus

Builds a Nexus file including information from the SETS block by listening to events.

CharSetNexusFileBuilder() - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.CharSetNexusFileBuilder

childHasFocus(Component) - Static method in class info.bioinfweb.commons.swing.SwingUtils

childHasFocus(Composite) - Static method in class info.bioinfweb.commons.swt.SWTUtils

clear() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment

clear() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment

clear() - Method in class info.bioinfweb.commons.collections.ListDecorator

clear() - Method in class info.bioinfweb.commons.collections.NonStoringCollection

clear() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList

clear() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation

clear() - Method in class info.bioinfweb.commons.io.IOProgressListenerVector

clear() - Method in class info.bioinfweb.commons.swing.ActionMap

clear() - Method in class info.bioinfweb.commons.swing.ListBackedListModel

clear() - Method in class info.bioinfweb.commons.text.UniqueNameMap

clearMessages() - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog

clearOffscreeImage() - Method in class info.bioinfweb.commons.applet.DoubleBufferedApplet

clone() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion

Returns a new instance if this class having the same version numbers and application type as this instance.

clone() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore

clone() - Method in class info.bioinfweb.commons.io.FormatVersion

close() - Method in class info.bioinfweb.commons.io.LimitedInputStream

Closes the decorated input stream, if that is currently allowed.

close() - Method in class info.bioinfweb.commons.io.LimitedReader

Closes the decorated reader, if that is currently allowed.

close() - Method in class info.bioinfweb.commons.io.PeekReader

close() - Method in class info.bioinfweb.commons.log.TextFileApplicationLogger

Closes the underlying writer or the target file.

CLOSING_TAG_PATTERN - Static variable in class info.bioinfweb.commons.HTMLTruncater

Checks for closing tags, allowing leading and ending space inside the brackets

ClosingNotAllowedException - Exception in info.bioinfweb.commons.io

This exception is thrown by LimitedReader or LimitedInputStream if their close() method is called while closing these streams is prohibited.

ClosingNotAllowedException() - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException

ClosingNotAllowedException(String, Throwable) - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException

ClosingNotAllowedException(String) - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException

ClosingNotAllowedException(Throwable) - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException

codeCorrect(String, String) - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement

codeToID(String) - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement

CollectionUtils - Class in info.bioinfweb.commons.collections

CollectionUtils() - Constructor for class info.bioinfweb.commons.collections.CollectionUtils

colorToHexString(Color) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils

columnAdded(TableColumnModelEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter

columnMarginChanged(ChangeEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter

columnMoved(TableColumnModelEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter

columnRemoved(TableColumnModelEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter

columnSelectionChanged(ListSelectionEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter

COMMAND_TERMINATOR - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer

COMMAND_TERMINATOR - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter

CommandLineReader - Class in info.bioinfweb.commons

Tool class that allows to analyze command line arguments that have been passed to an application.

CommandLineReader(String[]) - Constructor for class info.bioinfweb.commons.CommandLineReader

Creates a new instance of this class.

COMMENT_END - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter

COMMENT_START - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter

compare(T, T) - Method in class info.bioinfweb.commons.collections.SequenceIntervalPositionAdapterForComparable

compare(SimpleSequenceInterval, SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalFirstPosComparator

compare(SimpleSequenceInterval, SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalLastPosComparator

compare(SimpleSequenceInterval, SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter

compare(StreamLocationProvider, StreamLocationProvider) - Method in class info.bioinfweb.commons.io.StreamLocationProviderOffsetComparator

compare(AcceptLanguageEntry, AcceptLanguageEntry) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.QualityComparator

Returns -1 if o1.getQuality() is less than o2.getQuality(), 0 is they are equal and 1 if o1.getQuality() is greater than o2.getQuality().

compareTo(ApplicationVersion) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion

Compares two application versions.

compareTo(AmbiguityBaseScore) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore

compareTo(SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceInterval

compareTo(FormatVersion) - Method in class info.bioinfweb.commons.io.FormatVersion

Returns 0 if major and minor version are equal, 1 if this version is later than the specified one and -1 if the specified version is later.

complement(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

Returns the complement of the specified character.

complement(CharSequence) - Static method in class info.bioinfweb.commons.bio.SequenceUtils

Returns the complementing sequence.

ConcatenatedSequenceView<C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.views

Allows to view multiple concatenated sequences as a single sequence.

ConcatenatedSequenceView() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView

ConcatenatedSequenceView(Collection<Sequence<C>>) - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView

ConcatenatedSequenceView(Sequence<C>[]) - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView

ConcatenatedSequenceView(Sequence<C>) - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView

ConcatenatedSequenceView.ViewedSequence - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.views

concatWithOperator(String, String, String, String, String) - Static method in class info.bioinfweb.commons.text.StringUtils

Concatenates two expressions with an operator if both are not empty.

concatWithOperator(String, String, String) - Static method in class info.bioinfweb.commons.text.StringUtils

Concatenates two expressions with an operator if both are not empty.

ConcreteSQLProperties - Class in info.bioinfweb.commons.sql.sqlproperties

Default implementation of the SQLProperties interface.

ConcreteSQLProperties() - Constructor for class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties

ConsensusSequenceCreator - Class in info.bioinfweb.commons.bio

ConsoleApplicationLogger - Class in info.bioinfweb.commons.log

An implementation of ApplicationLogger that outputs all messages to System.out and System.err.

ConsoleApplicationLogger() - Constructor for class info.bioinfweb.commons.log.ConsoleApplicationLogger

consumeNewLine() - Method in class info.bioinfweb.commons.io.PeekReader

Consumes any one of a line feed '\n', a carriage return '\r', or a carriage return followed immediately by a line feed, if found at the current position of the reader.

contained(String, int, int) - Method in class info.bioinfweb.commons.CommandLineReader

Checks if the given value is contained in the arguments and returns the index.

contained(String, int) - Method in class info.bioinfweb.commons.CommandLineReader

Checks if the given value is contained in the arguments and returns the index.

contained(String) - Method in class info.bioinfweb.commons.CommandLineReader

Checks if the given value is contained in the arguments and returns the index.

contains(Object) - Method in class info.bioinfweb.commons.collections.ListDecorator

contains(int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList

Checks whether the specified position is marked by this list.

contains(Object) - Method in class info.bioinfweb.commons.collections.NonStoringCollection

Since no objects are stored in this collection this method will always return false.

contains(Object) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList

contains(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AccessibleUndoManager

contains(JFileChooser) - Method in class info.bioinfweb.commons.swing.FileChooserDirModel

containsAll(Collection<?>) - Method in class info.bioinfweb.commons.collections.ListDecorator

containsAll(int, int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList

Checks whether all positions in the specified interval are marked by this list.

containsAll(Collection<?>) - Method in class info.bioinfweb.commons.collections.NonStoringCollection

Since no objects are stored in this collection this method will always return false.

containsAll(Collection<?>) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList

containsAllNames(Collection<?>) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment

containsAllNames(Collection<?>) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment

containsKey(Object) - Method in class info.bioinfweb.commons.text.UniqueNameMap

containsName(String) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment

containsName(String) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment

containsPosition(int) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList

containsRect(Rectangle, Rectangle) - Static method in class info.bioinfweb.commons.Math2

Checks if one rectangle is completely contained inside the other.

containsValue(Object) - Method in class info.bioinfweb.commons.text.UniqueNameMap

containsWhitespace(CharSequence) - Static method in class info.bioinfweb.commons.text.StringUtils

Tests if the specified character sequence does not contain any whitespace.

ContentExtensionFileFilter - Class in info.bioinfweb.commons.io

An abstract file filter that allows to test the content of a file to determine whether it is accepted by this filter.

ContentExtensionFileFilter(String, boolean, ContentExtensionFileFilter.TestStrategy, boolean, String...) - Constructor for class info.bioinfweb.commons.io.ContentExtensionFileFilter

Creates a new instance of this class.

ContentExtensionFileFilter(String, boolean, String...) - Constructor for class info.bioinfweb.commons.io.ContentExtensionFileFilter

Creates a new instance of this class.

ContentExtensionFileFilter.TestStrategy - Enum in info.bioinfweb.commons.io

Determines the way instances of ContentExtensionFileFilter determine which files are valid.

convertCamelCase(String, String) - Static method in class info.bioinfweb.commons.text.StringUtils

Converts a camel case keyword to a string with the specified separator where all characters are in lower case.

CookieManager - Class in info.bioinfweb.commons.servlet

CookieManager() - Constructor for class info.bioinfweb.commons.servlet.CookieManager

copy(InputStream, OutputStream) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies data from an InputStream to an OutputStream.

copy(InputStream, OutputStream, boolean) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies data from an InputStream to an OutputStream.

copy(InputStream, OutputStream, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies data from an InputStream to an OutputStream.

copy(InputStream, OutputStream, boolean, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies data from an InputStream to an OutputStream.

copy(File, File, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies a file.

copy(File, File) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies a file.

copyBits(long, long, long) - Method in interface info.bioinfweb.commons.collections.bitstorage.BitField

Copies the specified number of bits from one position in the bit field to another.

copyFromResource(String, OutputStream) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies data from an InputStream to a OutputStream.

copyFromResource(String, OutputStream, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils

Copies data from an InputStream to a OutputStream.

CountableSequenceView - Interface in info.bioinfweb.commons.bio.biojava3.core.sequence.views

Should be implemented by all sequence views that e.g.

countChangedCompounds() - Method in interface info.bioinfweb.commons.bio.biojava3.core.sequence.views.CountableSequenceView

countChangedCompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView

countChangedCompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.UpperCaseSequenceView

countCompounds(C...) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView

createDecoratedListIterator(ListIterator<E>) - Method in class info.bioinfweb.commons.collections.ListDecorator

createEntry() - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement

createFont(double) - Method in class info.bioinfweb.commons.graphics.ZoomableFont

Creates a new Font instance according to the properties if this object and the provided zoom factor.

createID(Connection, String, String, int, int) - Static method in class info.bioinfweb.commons.sql.IDGenerator

Returns a random ID which is not contained in the specified column of the specified table by the time this method is called.

createID(Connection, String, String, long, long) - Static method in class info.bioinfweb.commons.sql.IDGenerator

Returns a random ID which is not contained in the specified column of the specified table by the time this method is called.

createID(Connection, String, String, String, int) - Static method in class info.bioinfweb.commons.sql.IDGenerator

Returns a random ID which is not contained in the specified column of the specified table by the time this method is called.

createIntListCond(String, List<Integer>, String) - Static method in class info.bioinfweb.commons.sql.SQLUtils

createLabelTable(int, int, double) - Method in class info.bioinfweb.commons.swing.DecimalInput

createNewID() - Method in class info.bioinfweb.commons.IntegerIDManager

Returns a new sequence identifier that has not been returned before.

createNewID() - Method in class info.bioinfweb.commons.LongIDManager

Returns a new sequence identifier that has not been returned before.

createNextID(Connection, String, String, boolean, int) - Static method in class info.bioinfweb.commons.sql.IDGenerator

Returns the next ID which is not already present in the specified table.

createNextID(Connection, String, String, boolean, long) - Static method in class info.bioinfweb.commons.sql.IDGenerator

Returns the next ID which is not already present in the specified table.

createRedoAction(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement

createUndoAction(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement

createURI(String) - Static method in class info.bioinfweb.commons.swing.actions.OpenWebsiteAction

cutEnd(CharSequence, int) - Static method in class info.bioinfweb.commons.text.StringUtils

Cuts off the specified number of characters from the end of the specified character sequence.

cutEnd(String, int) - Static method in class info.bioinfweb.commons.text.StringUtils

Cuts off the specified number of characters from the end of the specified string.

CYTOSINE_INDEX - Static variable in class info.bioinfweb.commons.bio.AmbiguityBaseScore

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